Mesial temporal lobe epilepsy is the most common form of partial epilepsy, and also the most drug-resistant. Hippocampal sclerosis is observed in the majority of drug-resistant mesial temporal lobe epilepsy patients, making it an important pathological biomarker in this disease, and possibly a valuable tool for deciphering disease pathophysiology. Understanding cell-specific processes that influence how genes are expressed in mesial temporal lobe epilepsy patients with and without the hippocampal pathology is an important step towards discovering the pathogenic processes involved. Accordingly, the goal of this application is to optimize and apply methodologies to investigate two key genomic processes (somatic mutations and mRNA expression) that may contribute to the development of hippocampal sclerosis. To do this, we first will optimize a novel next-generation sequencing method to sequence the transcriptome of small populations of dentate granule cells, a cellular population believed to be integrally involved in the development of hippocampal sclerosis. Second, we will evaluate variant calling accuracy of whole-genome next-generation sequencing protocols starting from minute amounts of genomic DNA procured from small numbers of homogenous cells to explore the feasibility of accurate detection of somatic variants. Finally, these methods will be applied to characterize the cellular transcriptome and somatic genome of dentate granule cells collected from a set of mesial temporal lobe epilepsy patients with hippocampal sclerosis compared to a set of patients without hippocampal sclerosis. If these methodologies can be optimized and applied in a way to be able to detect cell- specific genomic changes associated with the disease pathology, we will have valuable tools and the necessary preliminary data to design additional, more comprehensive genomic studies in mesial temporal lobe epilepsy. Secondarily, this work may also provide an important foundation to motivate the study of the cell- specific genome in other diseases where tissue specimens are available.